Different Species With The Same "Junk DNA"

The Short Summary

The example below shows that two patterns have been found in the
genetics of both cows and whales. Neither pattern is found in mice and
horses. This implies that cows and whales inherited them from a
common ancestor. I discuss how scientists checked if it was just a
coincidence.

The Basic Idea

Most of your DNA is "junk". We call it that because the DNA
sequence inside a "junk" region is never used to form a
protein. The junk isn't after a Start codon, or else is right after a
Stop codon, so the gene expression mechanisms simply never look at the
junk. They skip over it. There is also "junk" which is
inside a gene, but which is ignored when the gene is used. The details
are complicated, but if you are interested, see Section Two of this Talk.Origins
FAQ.

Junk DNA is inherited. Suppose we find a pattern in the junk DNA of
two different species, and don't find that pattern in other species.
Evolution can explain the situation by saying that the two species
recently had a common ancestor, and both species inherited this
pattern from their ancestor. In short, evolution suggests the family tree:

====================== species A without the pattern
|
common |
ancestor ======| ====== species B with the pattern
species | common |
of A, B and C ====ancestor===X===|
species |
of B and C ====== species C with the pattern

"X" marks where the pattern arose.

To the best of my knowledge, Creationism does not predict or
explain such situations. Since the pattern is in the junk, one cannot
argue that the pattern confers any short-term benefit or meets any need.

Of course, coincidences do happen. In the example below, I discuss
how scientists checked to see if the pattern they'd found was
meaningful or not.

An Example: Whales and Cows

You may have heard that the AIDS virus copies itself into its
host's DNA. It can do this because there is a "reverse
transcription" mechanism which leaves a so-called
retroposon at some randomly chosen place in your DNA. There is
a category of retroposon called a SINE (Short INterspersed
Element).

A recent study found two different SINEs were present in the
Hippopotamus, Cow, Sperm Whale, and Humpback Whale. Neither SINE was
in the Red Kangaroo, Human, Mouse, Cat, Asiatic Elephant, Domestic
Horse, Pig, or Bactrian Camel. This suggests the family tree

There are a number of ways to check if this is really the case.
The first question is whether the patterns are just some random
fluctuation of junk DNA. Randomness is ruled out for at least four different reasons.

Next, we have to ask if a retrovirus could have just infected
several species. This also can be ruled out.

Next, we ask if the conclusion is believable. Could a land animal
have evolved into a whale? The answer is that the land ancestry of
whales is a century-old idea, and well-proven without this new line of
evidence. The ancestry was originally suggested based on the fact that
whales are mammals, with a placenta and live birth and mother's
milk. The idea is confirmed (for example) by mitochondrial DNA
similarities, by protein similarities, and by fossils of small whales
with legs. Also, whales with vestigial hind legs are sometimes born.

Finally, we ask if this conclusion leads anywhere. To be science, it has to make predictions, that can
be tested to see if they are right.

The answer is yes. From the standard biological taxonomy, we can
predict that only artiodactyls ("even toed" mammals) have the
patterns. So, we can test animals that aren't artiodactyls, like cats
and iguanas. We can predict that since cows have the patterns, all
ruminants should. So, we can test sheep and goats. We predict
that all cetaceans have the patterns, so we can test dolphins
and killer whales. Furthermore, we don't predict just that dolphins
have the patterns. We also predict that dolphins have the patterns at
the exact same genetic locations.

In fact, many of these predictions have already been tested, and so
far they have always been correct.The Minke Whale, Baird's Beaked
Whale, Dall's Porpoise, Short-Finned Pilot Whale, and Bottlenose
Dolphin all had both patterns, and in exactly the predicted places.
Sheep, the Reticulated Giraffe, the Axis Deer, and the Lesser Malayan
Chevrotain also are as predicted.

To sum up: this evidence unambiguously says that whales and cows
have a common ancestor.

References:

Molecular evidence from retroposons that whales form a clade within
even-toed ungulates, Shimamura et al, Nature 388,666 (14
August 1997)

The diagram below shows the conclusions of the paper. This web
page has only mentioned two SINEs, which are marked as B and C on the
diagram. The article talks about nine SINEs, which allow us to
conclude (for instance) that the hippo is closely related to
whales. Which is not a surprise, since hippos can nurse infants
underwater, just like whales.

Phylogenetic relationships among cetartiodactyls based on
insertions of short and long interspersed elements: Hippopotamuses are
the closest extant relatives of whales, Nikaido, Rooney and Okada,
Proceedings
of the National Academy of Sciences 96, 10261 (31 August 1999)

This followup paper did a wider search, and found 20 independent
insertion events. Click on the diagram below to see its conclusions.

Footnotes:

Four reasons the patterns aren't random. First, the
patterns are too large to randomly occur several times. Second, they
were not found anywhere in the computer databases of previously known
DNA patterns, meaning that they aren't particularly probable. Third,
randomness should have caused creatures that had one pattern but not
the other. Fourth, they are found in the identical places on the
chromosomes of different species. Random things should occur in random
places. As the editors of Nature pointed out, the chance of two
such events happening at the same location is virtually nil. Yet the
patterns are found, not at one matching location, but at seven matching
locations. The overall coincidence is "virtually nil" to the
seventh power.

Reasons that retroviruses didn't just infect multiple
species. Cross-infection does happen. For example, AIDS is thought
to have jumped from monkeys to humans. However, cross-infection is
quite rare, and it only happens when the two target species share an
environment. Cows and humpback whales do not share an environment,
yet both have both patterns. Hippos and elephants do share some
environments, but one has both patterns and the other has neither
pattern. Cows and mice share some environments, but one has both patterns
and the other has neither.

Also, it is improbable that one virus could attack so many species
and yet be the same: it should have had to mutate into several
variants, as AIDS has. It is improbable that two viruses would both
succeed in spreading widely. It is improbable that both would attack
the identical set of targets.

But more importantly, if a retrovirus had infected multiple
species, it should have left itself in a different place in each
species. After all, leaving a pattern in junk DNA is an accident: a
virus "dies" as a result. In fact, in cows, one of the patterns
has been copied to five different places. Clearly, there is no single
place in the junk DNA where the pattern "should" be, or
"tries" to be. So, finding a pattern in the exact same place
(at the same genetic locus) in two species implies that the two
species inherited the pattern. Finding one pattern at the same place
in five different whales, a dolphin and a porpoise settles the
matter. That locus must have been affected once, in their common
ancestor.